updating free tagging

Thank you for development of such a good module! It's really useful to our team!
I found a bug about free tagging. When I import an Endnote XML file and assign taxonomy, that is perfect! But when I need to update taxonomy for a specific node, after submitting that, the value of taxonomy is empty! I don't know what causes this problem. I repeat this all the time. The setting of taxonomy is free tagging with hierarchy. But when I update nodes using taxonomy_multi_edit module, values are stored correctly. So I guess there might be something wrong updating taxonomy.
Thank you for your time and efforts!